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Data from: Observation of persister cell histories reveals diverse modes of survival in antibiotic persistence

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Mar 25, 2025 version files 1.13 MB

Abstract

Bacterial persistence is a phenomenon in which a small fraction of isogenic bacterial cells survives a lethal dose of antibiotics. Although the refractoriness of persistent cell populations has classically been attributed to the presence of growth-inactive cells generated prior to drug exposure, evidence is accumulating that actively growing cell fractions can also produce persister cells, depending on bacterial species, antibiotics, and culture conditions. However, the direct elucidation of survival modes, drug response diversity, and growth history dependence by single-cell observation is limited due to the extremely low frequencies of persisters. Here, we visualize the responses of more than 106 individual cells of wildtype Escherichia coli to lethal doses of antibiotics, sampling cells from different growth phases and culture media into a microfluidic device. We show that when cells sampled from exponentially growing cell populations in batch cultures were treated with ampicillin or ciprofloxacin, all persisters for which we identified their single-cell histories were growing prior to antibiotic treatment. We detected pre-existing growth-arrested non-growing persisters to ampicillin for an E. coli strain expressing a defective general stress response regulator, but these constituted minor fractions of persister cells. Growing persisters exhibit heterogeneous survival dynamics in response to drug exposure, including continuous growth and fission with L-form-like morphologies, responsive growth arrest, or post-exposure filamentation. Incubating cells under stationary phase conditions increases both the frequency and the probability of survival of non-growing persisters to ampicillin. However, no non-growing persisters were identified for ciprofloxacin treatment, even in post-stationary phase cell populations. These results demonstrate diverse persistence dynamics at the single-cell level depending on antibiotic types and the pre-exposure cultivation history.